Series creator Chris Carter believed that the show could continue for another ten years with new leads, and the opening credits were accordingly redesigned again. During the airing of season eight, Carter and The X-Files production team created and aired a spinoff titled The Lone Gunmen. The show was unsuccessful and was cancelled before any story arcs were resolved. The episode "Jump the Shark" was created to give closure to the series.

"The show has been Mulder's quest for the truth. It was that for seven years and for part of the eighth year. But I really think that with the introduction of John Doggett last year, [...] a baton was passed [...] literally he [Mulder] handed over the X-Files office to Doggett."

Hopeful about reuniting with Mulder, a complete stranger offers his service to drive Mulder out of hiding. Scully takes the offer, but unknowingly gets herself and Mulder in even more danger. The "Shadow Man" (Terry O'Quinn), a government agent, follows Scully. It is then discovered that he is a "Super Soldier" bent on killing Scully and Mulder. As confirmed in this episode, a "Super Soldier"'s only weakness is magnetite, which leads to the death of the "Shadow Man".[3] Later on, Scully, Doggett and Reyes find evidence of a dangerous UFO cult which has found a second spacecraft similar to one Scully studied in Africa two years ago (as seen in "The Sixth Extinction"). Misled by the FBI, the agents enlist the help of The Lone Gunmen to protect Scully's son after they learn that the UFO cult apparently intend to kill the child.[4] Doggett is run over by a car, leading him to be sent to the local hospital. As Follmer and the "Toothpick Man" (Alan Dale) are trying to uncover the plans of the three agents, Scully and Reyes leaves Washington, D.C. to find Scully's son.[5]

Doggett finds a strange disfigured man in the X-Files office; believing he is Mulder, they test his DNA. The test reveals him to have the same pattern as Mulder. The disfigured man sticks a needle into William, which the other agents believe to be a virus of some kind, but is later revealed to be a cure for William's powers. The unnamed man is later unveiled to be Jeffrey Spender (Chris Owens), Mulder's half-brother.[6] Mulder returns from hiding to only be discovered looking for classified information at an army base and, after allegedly killing an apparently indestructible "Super Soldier", he is placed on trial to defend the X-Files and himself. But with the help of Kersh, Scully, Reyes, Doggett, Spender, Marita Covarrubias (Laurie Holden) and Gibson Praise (Jeff Gulka), Mulder breaks out. Mulder and Scully travel to New Mexico to find an old "wise man", who is later revealed to be the "Cigarette Smoking Man" (William B. Davis). The Smoking Man is later killed by commands from Knowle Rohrer (Adam Baldwin). The series concludes with Skinner attempting to contact Kersh who has been forced to close down the X-Files. Doggett and Reyes are last seen driving off into the desert after aiding Mulder and Scully, who are now on the run from the FBI and are last seen together in a motel room facing an uncertain future.[7]

Before greenlighting a ninth season, neither the Fox Network nor any of the Ten Thirteen Productions members knew if creator Chris Carter would return for another season. While he encouraged the other members of the crew to continue the series without him, Carter was not sure. However, several crew members started to develop new scripts for the ninth season, which caused Carter to become more excited about the prospects of a new season.[2] At the last second, Carter signed a contract with Fox for another year.[8]

"Jump the Shark" served as the series finale of the cancelled X-Files spin-off series The Lone Gunmen. David Duchovny returned to the show, and the opening credits, for the two-part series finale, "The Truth". This is rare as most regulars who return to a show are usually billed as "Special Guest Stars." This also marks the most number of cast members to be featured in the opening credits of the show.[9]

The show's crew and actors had much to say about the finale, "The Truth". Chris Carter said of the finale, "It's the end – you don't get another chance. So you'd better put everything you've ever wanted to put in into the episode. There were things to distract from what was going on. The band was breaking up." Actress Annabeth Gish said, "It did feel like a big movie set. We were on location, there was an enormous budget, and everyone came back." William B. Davis said, "It was great that they brought us all back in the finale, that they found a way to get us all in again." Actor Mitch Pileggi said, "I can remember the last day on the set. We shot a scene with Gillian and myself, and that was it. And then I had to say goodbye to another family, another crew. I almost teared up, and Gillian was standing there looking at me saying 'Okay, go ahead, big guy; get through this.' It was tough." Robert Patrick said, "It was pretty euphoric, and sad, and all those emotions you can imagine. A chapter's closing, and we're all moving on to something new and exciting. And yet we were all going to miss each other." Kim Manners called the final scene "truly one of the most emotional experiences I've ever witnessed in my life."[10] Former lead actor Duchovny said, "In some ways, psychically I didn't really leave. It was nice to be able to – I'm just really happy that I was able to come back and finish it."[11]

After officially announcing that season nine would be the last of the series, Chris Carter and his crew opened negotiations with Duchovny. Initially, they were unsure if he would appear in the finale, since he directed and co-wrote "William". Duchovny later on decided to return to the show in the finale. Frank Spotnitz said, "My impression from talking to him was that he still cares about the show. He's still invested in it and certainly cares about [Mulder]. And I think he recognized that it was the best thing for the show and the audience [for him] to come back and give closure to nine years of the series."[14]

Series creator Chris Carter also served as executive producer and showrunner and wrote nine episodes, including the two-part season premiere and series finale, as well as important mytharc episodes. Frank Spotnitz continued as executive producer and wrote seven episodes, plus receiving story credit for an additional episode. Vince Gilligan continued as executive producer and wrote three episodes. John Shiban was promoted to executive producer and wrote two episodes, plus receiving story credit for an additional episode. David Amann was promoted to supervising producer and wrote two episodes. Steven Maeda was promoted to executive story editor and wrote two episodes. Former writer for The X-Files spin-off series The Lone GunmenThomas Schnauz joined the writing staff as a story editor and wrote two episodes. Cast member David Duchovny received story credit for a single episode.[16]

Kim Manners continued as co-executive producer and directed the most of episodes of the season with eight, including the two-part series finale. Tony Wharmby directed three episodes. Series creator Chris Carter directed two episodes. Co-executive producer Michelle MacLaren and series writer John Shiban each made their directorial debuts, directing one episode. Series writers Frank Spotnitz and Vince Gilligan each directed an episode, after previously directing their first episodes the previous season. The remaining episodes were directed by Dwight Little, Cliff Bole, and cast member David Duchovny.[16]

The first episode of the season, "Nothing Important Happened Today", gathered 10.6 million viewers, whereas the second part gathered only 9.4 million viewers.[17] On May 19, 2002, the series finale, "The Truth", aired, and the Fox Broadcasting Company confirmed that The X-Files was not being renewed for a tenth season.[12] When talking about the beginning of the ninth season, Chris Carter said, "We lost our audience on the first episode. It's like the audience had gone away, and I didn't know how to find them. I didn't want to work to get them back because I believed what we are doing deserved to have them back."[18] "The Truth" received the highest Nielsen household rating and viewership numbers of the season. It earned a 7.5 rating[19] and gathered 13.25 million viewers in the United States.[20] The loss of viewers in the ninth season resulted in a 30 percent drop in viewership when compared to the eighth season.[17]

Sabadino Parker from PopMatters, when commenting on the series finale, said, "It's also for the good, because The X-Files has long been but a pale reflection of the show it once was."[21] Brian Linder from IGN was more positive to the ninth season, saying that the series could still have aired if the writers created a new storyline for Robert Patrick and Annabeth Gish's character, which The X-Files crew did not do and continued what was seen by many critics as tiresome.[22] Aaron Kinney from Salon magazine was more negative to the new season, even joking about the new female lead, calling her a "peppy new female presence."[23]Entertainment Weekly reviewer Ken Tucker said the show operated in what he called "quaint territory", speculating that Chris Carter was the only one who seemed to understand the complex mytharc.[24] Elizabeth Weinbloom from The New York Times concluded with, "shoddy writing notwithstanding, it was this halfhearted culmination of what was once a beautifully complicated friendship", between Mulder and Scully, ended remaining interest in what was a "waning phenomenon".[25] Another review from The New York Times said of the show, "The most imaginative show on television has finally reached the limits of its imagination."[26]The A.V. Club listed the ninth season and the 2008 film The X-Files: I Want to Believe as the "bad apple" of The X-Files, describing the ninth season as "clumsy mish-mash of stuff that had once worked and new serialized storylines about so-called 'super soldiers'".[27]

*^Although only appearing in the two-part series finale, Duchovny is listed in the opening credits. He also has a small uncredited cameo in "William", and appears in archive footage in "Trust No 1" and "Jump the Shark".[15]

Shannon McMahon, a former Marine associate of Doggett's, reveals to Doggett that she is a "Super Soldier." This leads them to a clandestine laboratory where secret experiments are taking place aboard a naval ship.

Scully is hopeful about reuniting with Mulder when a complete stranger offers new information about what drove him into hiding. Yet her trust in the stranger may place Mulder in even more danger. The tagline of this episode is "They're Watching."

With no knowledge of his identity or his past, Doggett is found wandering a dusty Mexican town. While he struggles to piece together his memory, he finds himself embroiled in a smuggling plot. Across the border Scully and Reyes attempt to find him.

Reyes takes the lead while investigating an X-File case surrounding a man found skinned alive. When she discovers that he had visions of a similar thing, she calls on Scully's expertise to help with the investigation.

Awakening in a surreal hospital – which a companion believes to be Death's Waiting Room – after being hit by a car, a comatose Reyes struggles to wake herself up before her organ donor card is acted upon.

When Morris Fletcher approaches the agents with information related to the "Super Soldiers", they turn to The Lone Gunmen. But the Gunmen are already knee-deep in a bio-terrorist's plot which has links to the mysterious Yves Adele Harlow.

Doggett finds a strange, disfigured man in the X-Files office and, on a whim of Scully's, they test his DNA. The surprising answers they find become even more surprising when William's life is put on the line.

After not knowing Mulder's whereabouts for the last year, Skinner and Scully learn he's being held for the murder of a military man he couldn't possibly have killed: Knowle Rohrer (Adam Baldwin), one of the government's secret "Super Soldiers." Mulder breaks out of prison with help of Skinner, Reyes, Doggett, Scully and Alvin Kersh. Mulder and Scully travel to New Mexico where Black helicopters destroy an Anasazi cliff dwelling ruin along with the Cigarette Smoking Man (William B. Davis).